AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i228_6_1_1_17_ecoli_hinf_reg_100.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -x5 Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 gltX 258 glutamate tRNA synthetase, catalytic subunit #2 HI0274 300 glutamyl-tRNA synthetase (gltX) Motif number 1 GGAGTCGCATTATAGGGAGAGTTCAAAATG 1 20 1 TATAGGGAGA 0.955217 -239 TTGAGGAATCAGGCGGGAGTGATAGAATAT 1 176 1 AGGCGGGAGT 0.982088 -83 TGGAAAAATTAAGTGGGCGATATTCTATCA 1 195 0 AAGTGGGCGA 0.990628 -64 AAGTTTGACCAAGCGGGCGATTAGC 2 6 0 AAGCGGGCGA 0.99129 -295 TTTAGAGAAGTGGTGGGCGATACCGGTCTC 2 55 1 TGGTGGGCGA 0.990522 -246 CTCCCTTACAAGGAGGGGGTCACTGGTTCG 2 84 0 AGGAGGGGGT 0.958156 -217 CGATTAGCTCAGTTGGGAGAGCACCTCCCT 2 108 0 AGTTGGGAGA 0.981908 -193 GGGTTGGCATTATAGGGAGAATGCATTTTC 2 151 1 TATAGGGAGA 0.955217 -150 ********** Masking position 5 Map Score: 13.5455 Number of sites scoring better than the average of aligned sites = 510 Number in coding regions = 471 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 2 GATCATCTTGCTTAAATTTACGACGAACGAACA 1 74 0 CTTATTTACA 0.996229 -185 ATATCGCCCACTTAATTTTTCCAGGATTTGCCG 1 202 1 CTTATTTTCA 0.9877 -57 GAAATGGCCTTACGTTTAGAAAGATGCCGAC 1 238 0 CTTATTTAGA 0.986848 -21 AAAAAGTTTTCTTAATTTTACTAAGTTTGACCA 2 25 0 CTTATTTACA 0.996229 -276 GGATTTTATGCTTATTTTTACGACAATTAAACA 2 205 0 CTTATTTACA 0.996229 -96 **** ***** * Masking position 7 Map Score: 8.59725 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 7 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 3 AACTCTCCCTATAATGCGACTCCACACAGC 1 13 0 ATAATGCGAC 0.956845 -246 GGGAGAGTTCAAAATGAGTCAACGCATTTT 1 34 1 AAAATGAGTC 0.881108 -225 ATTTCTTTAGAAAATGCGTTGACTCATTTT 1 44 0 AAAATGCGTT 0.983994 -215 TTTCGTTGACAAATTGCGCAACACGGTCTG 1 113 0 AAATTGCGCA 0.901319 -146 AACGAAAACAATAATGCGTAAGGTAGAAAC 1 136 1 ATAATGCGTA 0.974569 -123 CATTCTCCCTATAATGCCAACCCACAACAT 2 144 0 ATAATGCCAA 0.797923 -157 GTATTGACTGAAAATGCATTCTCCCTATAA 2 160 0 AAAATGCATT 0.88857 -141 AAATAAGCATAAAATCCGCTTTTTTATTTA 2 221 1 AAAATCCGCT 0.894017 -80 ********** Masking position 3 Map Score: 4.94445 Number of sites scoring better than the average of aligned sites = 914 Number in coding regions = 765 Number in noncoding regions = 149 Number of orfs with sites within 600 bp upstream = 167 Fraction of orfs with sites within 600 bp upstream = 0.026823 Motif number 4 ATTTAAGCAAGATGATCGCAAAACAGACCG 1 90 1 GATGATCGCA 0.97681 -169 GGGAGTGATAGAATATCGCCCACTTAATTT 1 190 1 GAATATCGCC 0.978102 -69 GCTAATCGCCCGCTTGGTCA 2 1 1 GCTAATCGCC 0.996594 -300 TCCCAACTGAGCTAATCGCCCTTAATGTTG 2 120 1 GCTAATCGCC 0.996594 -181 ********** Masking position 5 Map Score: 4.0621 Number of sites scoring better than the average of aligned sites = 387 Number in coding regions = 377 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 5 ACGCATTTTCTAAAGAAATTGTTCGTTCGTC 1 55 1 TAAAGAAATG 0.917091 -204 GTCGTAAATTTAAGCAAGATGATCGCAAAAC 1 83 1 TAAGCAAGTG 0.973285 -176 GGCCTTACGTTTAGAAAGATGCCGACAACCG 1 233 0 TTAGAAAGTG 0.944779 -26 TTAGTAAAATTAAGAAAACTTTTTAGAGAAG 2 34 1 TAAGAAAATT 0.892252 -267 AGAAAACTTTTTAGAGAAGTGGTGGGCGATA 2 46 1 TTAGAGAATG 0.866592 -255 CCCCTCCTTGTAAGGGAGGTGCTCTCCCAAC 2 96 1 TAAGGGAGTG 0.946832 -205 AAACAAAATTTAATAAAAAGGTATTGACTGA 2 179 0 TAATAAAAGG 0.760768 -122 TTACGACAATTAAACAAAATTTAATAAAAAG 2 190 0 TAAACAAATT 0.685352 -111 GACTTCTAAATAAAAAAGCGGATTTTATGCT 2 226 0 TAAAAAAGGG 0.911853 -75 ******** ** Masking position 7 Map Score: 2.92274 Number of sites scoring better than the average of aligned sites = 869 Number in coding regions = 707 Number in noncoding regions = 162 Number of orfs with sites within 600 bp upstream = 173 Fraction of orfs with sites within 600 bp upstream = 0.0277867 Motif number 6 TATAATGCGACTCCACACAGCGG 1 4 0 CTCCACACAG 0.979441 -255 GCAAGATGATCGCAAAACAGACCGTGTTGC 1 96 1 CGCAAAACAG 0.980163 -163 TGACAAATTGCGCAACACGGTCTGTTTTGC 1 107 0 CGCAACACGG 0.964992 -152 AGAAAGATGCCGACAACCGGCAAATCCTGG 1 222 0 CGACAACCGG 0.949972 -37 AGACCGGTATCGCCCACCACTTCTCTAAAA 2 54 0 CGCCCACCAC 0.95806 -247 CGATACCGGTCTCGAACCAGTGACCCCCTC 2 72 1 CTCGAACCAG 0.960382 -229 GGGAGGTGCTCTCCCAACTGAGCTAATCGC 2 109 1 CTCCCAACTG 0.935403 -192 ********** Masking position 8 Map Score: 4.25805 Number of sites scoring better than the average of aligned sites = 2802 Number in coding regions = 2695 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 7 GTTCAAAATGAGTCAACGCATTTTCTAAAG 1 40 1 AGTCAACGCA 0.988797 -219 TTGCGCAATTTGTCAACGAAAACAATAATG 1 122 1 TGTCAACGAA 0.982781 -137 CTCCCTATAATGCCAACCCACAACATTAAG 2 140 0 TGCCAACCCA 0.980945 -161 TTTATTTAGAAGTCAAACAAGTCGTAGTAG 2 243 1 AGTCAAACAA 0.934928 -58 ********** Masking position 5 Map Score: 0.790315 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 73 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 8 ********** No masking Map Score: 8.40873e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 9 ********** No masking Map Score: 8.40873e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 10 ********** No masking Map Score: 8.40873e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0